[2024-01-24 12:39:35,559] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:35,564] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:35,564] [INFO] DQC Reference Directory: /var/lib/cwl/stgdecba160-3d0f-499f-aac4-5fc793494735/dqc_reference
[2024-01-24 12:39:36,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:36,751] [INFO] Task started: Prodigal
[2024-01-24 12:39:36,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg94b82113-c630-4677-a263-b256a8c8faea/GCF_020616595.1_ASM2061659v1_genomic.fna.gz | prodigal -d GCF_020616595.1_ASM2061659v1_genomic.fna/cds.fna -a GCF_020616595.1_ASM2061659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:38,875] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:38,876] [INFO] Task started: HMMsearch
[2024-01-24 12:39:38,876] [INFO] Running command: hmmsearch --tblout GCF_020616595.1_ASM2061659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdecba160-3d0f-499f-aac4-5fc793494735/dqc_reference/reference_markers.hmm GCF_020616595.1_ASM2061659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:39,108] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:39,110] [INFO] Found 6/6 markers.
[2024-01-24 12:39:39,127] [INFO] Query marker FASTA was written to GCF_020616595.1_ASM2061659v1_genomic.fna/markers.fasta
[2024-01-24 12:39:39,128] [INFO] Task started: Blastn
[2024-01-24 12:39:39,128] [INFO] Running command: blastn -query GCF_020616595.1_ASM2061659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdecba160-3d0f-499f-aac4-5fc793494735/dqc_reference/reference_markers.fasta -out GCF_020616595.1_ASM2061659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:39,718] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:39,722] [INFO] Selected 26 target genomes.
[2024-01-24 12:39:39,722] [INFO] Target genome list was writen to GCF_020616595.1_ASM2061659v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:39,745] [INFO] Task started: fastANI
[2024-01-24 12:39:39,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg94b82113-c630-4677-a263-b256a8c8faea/GCF_020616595.1_ASM2061659v1_genomic.fna.gz --refList GCF_020616595.1_ASM2061659v1_genomic.fna/target_genomes.txt --output GCF_020616595.1_ASM2061659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:39:48,825] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:48,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdecba160-3d0f-499f-aac4-5fc793494735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:39:48,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdecba160-3d0f-499f-aac4-5fc793494735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:39:48,834] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:39:48,834] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:39:48,835] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Lentilactobacillus laojiaonis	strain=IM3328	GCA_020616595.1	2883998	2883998	type	True	100.0	413	414	95	conclusive
Lentilactobacillus curieae	strain=CCTCC M 2011381	GCA_000785105.2	1138822	1138822	type	True	79.9275	74	414	95	below_threshold
Lentilactobacillus kribbianus	strain=YH-lac9	GCA_013184075.1	2729622	2729622	type	True	78.8841	100	414	95	below_threshold
Lentilactobacillus hilgardii	strain=ATCC 8290	GCA_000159315.1	1588	1588	type	True	78.6814	51	414	95	below_threshold
Lentilactobacillus diolivorans	strain=DSM 14421	GCA_001434255.1	179838	179838	type	True	78.4727	61	414	95	below_threshold
Lentilactobacillus hilgardii	strain=DSM 20176	GCA_001434655.1	1588	1588	type	True	78.3979	54	414	95	below_threshold
Lentilactobacillus senioris	strain=DSM 24302	GCA_001436555.1	931534	931534	type	True	78.332	100	414	95	below_threshold
Lentilactobacillus kosonis	strain=NBRC111893	GCA_003864335.1	2810561	2810561	type	True	78.3289	86	414	95	below_threshold
Lentilactobacillus senioris	strain=JCM 17472	GCA_001312065.1	931534	931534	type	True	78.3065	97	414	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:39:48,836] [INFO] DFAST Taxonomy check result was written to GCF_020616595.1_ASM2061659v1_genomic.fna/tc_result.tsv
[2024-01-24 12:39:48,838] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:39:48,838] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:39:48,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdecba160-3d0f-499f-aac4-5fc793494735/dqc_reference/checkm_data
[2024-01-24 12:39:48,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:39:48,857] [INFO] Task started: CheckM
[2024-01-24 12:39:48,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020616595.1_ASM2061659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020616595.1_ASM2061659v1_genomic.fna/checkm_input GCF_020616595.1_ASM2061659v1_genomic.fna/checkm_result
[2024-01-24 12:40:03,822] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:03,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:03,843] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:03,844] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:03,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020616595.1_ASM2061659v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:03,844] [INFO] Task started: Blastn
[2024-01-24 12:40:03,844] [INFO] Running command: blastn -query GCF_020616595.1_ASM2061659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdecba160-3d0f-499f-aac4-5fc793494735/dqc_reference/reference_markers_gtdb.fasta -out GCF_020616595.1_ASM2061659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:04,624] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:04,630] [INFO] Selected 31 target genomes.
[2024-01-24 12:40:04,630] [INFO] Target genome list was writen to GCF_020616595.1_ASM2061659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:04,649] [INFO] Task started: fastANI
[2024-01-24 12:40:04,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg94b82113-c630-4677-a263-b256a8c8faea/GCF_020616595.1_ASM2061659v1_genomic.fna.gz --refList GCF_020616595.1_ASM2061659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020616595.1_ASM2061659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:17,922] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:17,932] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:40:17,932] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000785105.2	s__Lentilactobacillus curieae	79.7441	74	414	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184075.1	s__Lentilactobacillus kribbianus	78.946	101	414	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159315.1	s__Lentilactobacillus hilgardii	78.6814	51	414	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.37	96.88	0.92	0.87	10	-
GCF_001434255.1	s__Lentilactobacillus diolivorans	78.4727	61	414	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.05	98.10	0.95	0.90	3	-
GCF_002993965.1	s__Apilactobacillus timberlakei	78.4182	69	414	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.96	98.30	0.93	0.87	9	-
GCF_001436555.1	s__Lentilactobacillus senioris	78.332	100	414	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.88	99.77	1.00	1.00	3	-
GCF_003864335.1	s__Lentilactobacillus curieae_A	78.3289	86	414	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281175.1	s__Apilactobacillus apinorum	78.233	61	414	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434135.1	s__Lentilactobacillus kisonensis	78.1947	50	414	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.52	0.95	0.93	3	-
GCF_005930975.1	s__Apilactobacillus kunkeei_E	78.0132	52	414	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:17,934] [INFO] GTDB search result was written to GCF_020616595.1_ASM2061659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:17,935] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:17,939] [INFO] DFAST_QC result json was written to GCF_020616595.1_ASM2061659v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:17,939] [INFO] DFAST_QC completed!
[2024-01-24 12:40:17,939] [INFO] Total running time: 0h0m42s